[ome-users] OMERO Import issues...

Wed Sep 23 16:28:28 BST 2009

I'm using a 64 bit distro so just made my java heap size like 6 GB's---

I'll have to double check my images-- they were just 16 megapixels (4k*4k)
image tiles I had alreaduy converted from tiff--> JPG to hopefully resolve
some of the issues I had been having...

But still seemed to choke-- this time I was able to get them to import, but
when I actually tried to load them through the webclient, it just kept
displaying a "no image" tag for the thumbail.. kind of odd

dg

On Wed, Sep 23, 2009 at 11:25 AM, Curtis Rueden <ctrueden at wisc.edu> wrote:

> Hi Björn & David,
>
> Thanks for the feedback, and sorry for your trouble importing large image
> planes. As of Beta 4.0.3, the OMERO.importer defaults to a maximum heap size
> of 1024 MB. So any image planes of 1 GB or more are certainly too large to
> process successfully, and even image planes over 512 MB may have problems
> due to temporary overhead or garbage collection issues.
>
> One workaround is to increase the maximum heap size. With a 32-bit JVM,
> this limit can often be 1536 or even ~1800 GB depending on your operating
> system. The process for increasing the heap size is platform-dependent,
> however. For example, on Mac OS X, right click the OMERO.importer icon,
> choose "Show package contents," navigate into Contents, and edit the
> Info.plist file's line "-Xmx1024M" to read "-Xmx1700M" or whatever value you
> wish to try.
>
> That said, we have plans to improve the support for large image planes by
> processing them in tiles, negating the need for such a large amount of RAM
> at once. Unfortunately, this support is not planned until at least Beta 4.2.
> The Bio-Formats readers already support processing an image plane in tiles,
> but the writers do not, so the bfconvert command line tool does not yet
> support this either.
>
> -Curtis
>
>
> On Wed, Sep 23, 2009 at 3:28 AM, Björn Quast <bquast at evolution.uni-bonn.de
> > wrote:
>
>> Hi David,
>>
>> I have had the same importing problems with one layer tif images, when
>> they
>> exceed a specific image size . There is no problem to import very large
>> multi-
>> layer tifs (about 500 Mb), but if one layer is to large the import stopped
>> and
>> I got a message on the console, that the java heap memory was exceeded.
>> I can only guess, that the importer fails to read in large strips of image
>> data. tif files may store all image data in one chunk or line by line or
>> in
>> smaller pieces. But even with line by line stored images I got the
>> problems,
>> if one layer is to large.
>>
>> It also happens, that a few images were imported but than the importer
>> stops.
>> Again, I can only guess that there is a memory issue.
>>
>> In the moment I can not reproduce it, because I have no omero running, but
>> perhaps I can give more details when my server is up again.
>>
>> Björn
>>
>> David Gutman wrote:
>> > I am having a lot of problems trying to import images into OMERO.    I
>> > am using the 4.0.3beta code and having issues trying to import any of
>> > my images.....
>> >
>> > The images are initially acquired as Aperio SVS files ....they are
>> > basically a TIFF container with JPEG2000 tiles embedded in them.
>> > I've tried the following scenarios and still can't get all of my
>> > images to consistently  import, and get all sorts of errors, so wanted
>> > to see if the community had any thoughts...
>> >
>> > 1) Split 6 channel SVS file into individual channels using
>> > tiffsplit--- these images are just standard tiff's, and I can even
>> > view them with imagemagick, and other graphics viewers (At least the
>> > small ones)
>> >    This produces 6 images, the really small images seem to import okay
>> > sometimes, but not always (like 1024x512 or whatever-- these generally
>> > are just an image of the label on the slide)...
>> >
>> > So some of the frames, but of course not the large frames (22090x27696
>> > pixels) will not load either through the GUI or through the command
>> > line interpreter--- I've restricted this now where I don't even try to
>> > upload images greater than 250 MegaPixels (so well under 1Gigapixel
>> > even considering all three channels) ......but I've had issues with
>> > even much smaller images....
>> >
>> > Has anyone had any similar issues trying to load in large files with
>> > the current beta of OMERO  I've even tried to transcode some of these
>> > using the bioformats tools to  OME-XML.TIFF files with similar
>> > disappointing results
>> >
>> > Oddly-- some of my images upload OK, and some do not...
>> >
>> > 2966455 2009-09-16 13:57 TCGA-06-0214-01B-03-BS3aad.tif
>> > 158051 2009-09-16 13:57 TCGA-06-0214-01B-03-BS3aab.tif
>> >
>> > The "b" image loaded fine, the "d" image did not-- it's not a terribly
>> > big image, but I keep getting weird errors when I try and import it--
>> > has anyone had any issues lately with the OMEROIMPORTER function/gui?
>>
>> --
>> Dr. Björn Quast
>> Universität Bonn
>> Institut für Evolutionsbiologie und Ökologie
>> 53121 Bonn
>> Tel.: 0228/735758   email: bquast at evolution.uni-bonn.de
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>
>

-- 
David A Gutman, M.D. Ph.D.
Center for Comprehensive Informatics
Emory University School of Medicine
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